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<a href="#pub-types">Public Types</a> &#124;
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<p>SubstitutionMatrix scores alignments using a residue type matrix such as BLOSUM62 or PAM250.  
 <a href="classmoltk_1_1SubstitutionMatrix__.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="SubstitutionMatrix_8hpp_source.html">SubstitutionMatrix.hpp</a>&gt;</code></p>
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Collaboration diagram for moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;:</div>
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<div class="center"><img src="classmoltk_1_1SubstitutionMatrix____coll__graph.png" border="0" usemap="#moltk_1_1SubstitutionMatrix___3_01SCORE__TYPE_01_4_coll__map" alt="Collaboration graph"/></div>
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<p><a href="classmoltk_1_1SubstitutionMatrix__-members.html">List of all members.</a></p>
<table class="memberdecls">
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; SCORE_TYPE &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef std::vector&lt; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#af8be0449f53b3a6fccffa510be56f528">MatrixType</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#adad5f64fb51e6d416823c831f9ebdfc4">SubstitutionMatrix_</a> (const std::string &amp;matrix_string, double bits_per_entry=1.0)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#ad203d839a955f6cf1e2346993a7f6da8">SubstitutionMatrix_</a> (std::istream &amp;matrix_stream, double bits_per_entry=1.0)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::istream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a2e2383d4b434b8c15ae55305a5e669fe">load_stream</a> (std::istream &amp;, double bits_per_entry=1.0)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a4eb58b41b9fef4021dd842b463d5d479">score</a> (char residue1, char residue2) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Look up score of two residue one-letter-codes in the matrix.  <a href="#a4eb58b41b9fef4021dd842b463d5d479"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#accd89e9d75caf9ec7146c670c49687aa">operator[]</a> (size_t ix) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Get matrix row by integer index.  <a href="#accd89e9d75caf9ec7146c670c49687aa"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#ac8bb03143da135cc66c82a09a7c71daf">operator[]</a> (char c) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Get matrix row by integer index.  <a href="#ac8bb03143da135cc66c82a09a7c71daf"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a09385778cece4012604101127eb1942b">size</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Number of rows in substitution matrix.  <a href="#a09385778cece4012604101127eb1942b"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const std::vector&lt; int &gt; &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#aaf02c227d0a4a121f69a8d46b7508f2f">get_character_indices</a> () const </td></tr>
<tr><td colspan="2"><h2><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a6983f87322f30d2e6578dc312855559d">get_blosum62</a> ()</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">static const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#aaee610797c7e81fa79cf654eb719579c">get_pam250</a> ()</td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#af8be0449f53b3a6fccffa510be56f528">MatrixType</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a414f1e260f700d726aa9970af5edbd5c">matrix</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; int &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a1f1a2d056adae546b8c191c37da99059">character_indices</a></td></tr>
<tr><td colspan="2"><h2><a name="friends"></a>
Friends</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::istream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a41e5684e9467675a5d91455ea0d07bbd">operator&gt;&gt;</a> (std::istream &amp;is, <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a> &amp;scorer)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Read a string representation of a SubstitutionMatrix from a C++ stream.  <a href="#a41e5684e9467675a5d91455ea0d07bbd"></a><br/></td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><h3>template&lt;class SCORE_TYPE&gt;<br/>
class moltk::SubstitutionMatrix_&lt; SCORE_TYPE &gt;</h3>

<p>SubstitutionMatrix scores alignments using a residue type matrix such as BLOSUM62 or PAM250. </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="af8be0449f53b3a6fccffa510be56f528"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::MatrixType" ref="af8be0449f53b3a6fccffa510be56f528" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">typedef std::vector&lt;<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a>&gt; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#af8be0449f53b3a6fccffa510be56f528">MatrixType</a></td>
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<a class="anchor" id="a5355d273a0a93e5ca33524f7b1d4ddb7"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::RowType" ref="a5355d273a0a93e5ca33524f7b1d4ddb7" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">typedef std::vector&lt;SCORE_TYPE&gt; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a></td>
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<hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="adad5f64fb51e6d416823c831f9ebdfc4"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::SubstitutionMatrix_" ref="adad5f64fb51e6d416823c831f9ebdfc4" args="(const std::string &amp;matrix_string, double bits_per_entry=1.0)" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a> </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>matrix_string</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">double&#160;</td>
          <td class="paramname"><em>bits_per_entry</em> = <code>1.0</code>&#160;</td>
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        <tr>
          <td></td>
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          <td></td><td><code> [explicit]</code></td>
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<a class="anchor" id="ad203d839a955f6cf1e2346993a7f6da8"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::SubstitutionMatrix_" ref="ad203d839a955f6cf1e2346993a7f6da8" args="(std::istream &amp;matrix_stream, double bits_per_entry=1.0)" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a> </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
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          <td class="paramkey"></td>
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<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a6983f87322f30d2e6578dc312855559d"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::get_blosum62" ref="a6983f87322f30d2e6578dc312855559d" args="()" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">static const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a>&amp; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::get_blosum62 </td>
          <td>(</td>
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          <td><code> [static]</code></td>
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<a class="anchor" id="aaf02c227d0a4a121f69a8d46b7508f2f"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::get_character_indices" ref="aaf02c227d0a4a121f69a8d46b7508f2f" args="() const " -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">const std::vector&lt;int&gt;&amp; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::get_character_indices </td>
          <td>(</td>
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<a class="anchor" id="aaee610797c7e81fa79cf654eb719579c"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::get_pam250" ref="aaee610797c7e81fa79cf654eb719579c" args="()" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">static const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a>&amp; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::get_pam250 </td>
          <td>(</td>
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<a class="anchor" id="a2e2383d4b434b8c15ae55305a5e669fe"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::load_stream" ref="a2e2383d4b434b8c15ae55305a5e669fe" args="(std::istream &amp;, double bits_per_entry=1.0)" -->
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          <td class="memname">std::istream&amp; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::load_stream </td>
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          <td class="paramtype">double&#160;</td>
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<a class="anchor" id="accd89e9d75caf9ec7146c670c49687aa"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::operator[]" ref="accd89e9d75caf9ec7146c670c49687aa" args="(size_t ix) const " -->
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          <td class="memname">const <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a5355d273a0a93e5ca33524f7b1d4ddb7">RowType</a>&amp; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::operator[] </td>
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<p>Get matrix row by integer index. </p>

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          <td>(</td>
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<p>Get matrix row by integer index. </p>

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<a class="anchor" id="a4eb58b41b9fef4021dd842b463d5d479"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::score" ref="a4eb58b41b9fef4021dd842b463d5d479" args="(char residue1, char residue2) const " -->
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          <td></td>
          <td>)</td>
          <td></td><td> const</td>
        </tr>
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<div class="memdoc">

<p>Look up score of two residue one-letter-codes in the matrix. </p>

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<a class="anchor" id="a09385778cece4012604101127eb1942b"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::size" ref="a09385778cece4012604101127eb1942b" args="() const " -->
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template&lt;class SCORE_TYPE&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname">size_t <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::size </td>
          <td>(</td>
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          <td> const<code> [inline]</code></td>
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<p>Number of rows in substitution matrix. </p>

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<hr/><h2>Friends And Related Function Documentation</h2>
<a class="anchor" id="a41e5684e9467675a5d91455ea0d07bbd"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::operator&gt;&gt;" ref="a41e5684e9467675a5d91455ea0d07bbd" args="(std::istream &amp;is, SubstitutionMatrix_ &amp;scorer)" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">std::istream&amp; operator&gt;&gt; </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>is</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt; &amp;&#160;</td>
          <td class="paramname"><em>scorer</em>&#160;</td>
        </tr>
        <tr>
          <td></td>
          <td>)</td>
          <td></td><td><code> [friend]</code></td>
        </tr>
      </table>
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<p>Read a string representation of a SubstitutionMatrix from a C++ stream. </p>

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</div>
<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="a1f1a2d056adae546b8c191c37da99059"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::character_indices" ref="a1f1a2d056adae546b8c191c37da99059" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">std::vector&lt;int&gt; <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a1f1a2d056adae546b8c191c37da99059">character_indices</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
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<a class="anchor" id="a414f1e260f700d726aa9970af5edbd5c"></a><!-- doxytag: member="moltk::SubstitutionMatrix_::matrix" ref="a414f1e260f700d726aa9970af5edbd5c" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
      <table class="memname">
        <tr>
          <td class="memname"><a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#af8be0449f53b3a6fccffa510be56f528">MatrixType</a> <a class="el" href="classmoltk_1_1SubstitutionMatrix__.html">moltk::SubstitutionMatrix_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1SubstitutionMatrix__.html#a414f1e260f700d726aa9970af5edbd5c">matrix</a><code> [protected]</code></td>
        </tr>
      </table>
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<div class="memdoc">

</div>
</div>
<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="SubstitutionMatrix_8hpp_source.html">SubstitutionMatrix.hpp</a></li>
</ul>
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